Shulou(Shulou.com)06/01 Report--

This article is to share with you about the use of TargetScan databases. The editor thinks it is very practical, so share it with you as a reference and follow the editor to have a look.

MiRNA in mammals plays a post-transcriptional regulatory role by binding to the 3 'UTR region of the transcriptional sequence. TargetScan is a special software for analyzing mammalian miRNA target genes, and has been compiled into a database based on the existing analysis results.

Http://www.targetscan.org/vert_72/

According to different representative species, it is divided into the following sub-databases

TargetScanHuman

TargetScanMouse

TargetScanFly

TargetScanWorm

TargetScanFish

Before predicting the target gene of miRNA, we first need to determine the 3'UTR region of the transcript. The database uses a sequencing technique called 3P-seq to determine the corresponding 3 'UTR region of the transcript. The principle of this technique is as follows

Combined with the analysis results of this technology and the existing 3'UTR annotations in NCBI, a comprehensive 3'UTR region sequence is provided.

We all know that miRNA is conservative among different species. by predicting the miRNA target sites of different species, targetscan's development team found that its binding sites are also conservative and can be divided into the following categories.

Further, according to the specific binding region and the multi-sequence alignment results of miRNA, it is divided into different miRNA family. The miRNA family information collated by targetscan can be queried through the following link

Http://www.targetscan.org/cgi-bin/targetscan/vert_72/mirna_families.cgi?db=vert_72&species=Human

According to the conservatism of sequences among different species, miRNA family is divided into the following four categories.

Broadly conserved

Conserved

Poorly conserved

Other mirbase annotations

Take TargetScanHuman as an example, the search interface is as follows

The database also contains miRNA target gene information of other species, such as mouse, so are the mouse miRNA target gene information queried in TargetScanHuman and TartgetScanMouse consistent?

Of course, it is inconsistent, the official saying is that the way to determine the 3'UTR region in the two databases is different, for the human in TargetScanhuman, the 3'UTR region of human is directly used, for mouse, the 3'UTR region is determined by homologous sequence alignment, the 3'UTR sequence of human is compared with the transcript of mouse, and the alignment region is the 3 'UTR region of mouse.

For the search function, there are three uses

1. Search gene

Both gene symbol and Emsembl id formats are supported. The search results are as follows

The corresponding transcripts of this gene and the corresponding length of 3 'UTR are given. Click on each transcript ID to view the miRNA binding sites on the transcript.

2. Retrieve transcript

Emsembl transcript id is supported, and the search results are as follows

First of all, a diagram is used to describe the miRNA binding sites on the transcript, and the specific binding region information is shown in a table, as shown below.

3. Retrieve miRNA

The search is based on the name of miRNA family, and the results are as follows

In addition to online search, the official website also provides a download function, as well as data and software, with the following links

Http://www.targetscan.org/cgi-bin/targetscan/data_download.vert72.cgi

Through TargetScan, we can easily retrieve the information of miRNA target genes in mammals.

Thank you for reading! This is the end of this article on "what's the use of TargetScan database?". I hope the above content can be helpful to you, so that you can learn more knowledge. if you think the article is good, you can share it for more people to see!

Welcome to subscribe "Shulou Technology Information " to get latest news, interesting things and hot topics in the IT industry, and controls the hottest and latest Internet news, technology news and IT industry trends.